How to achieve clean Topology at joining edge of dissimilar features?
In Blender most of us would not model a screw by joining two separate meshes, one for the curvature and the other for the groove. 

Other 3d packages such as AutoCAD / SolidWorks (and free alternatives) have a different internal representation of shapes. That's why boolean 'carving' is great for those kinds of programs. In those packages geometry remains a mathematical entity until converted to mesh-geometry for export. 

In Blender we use mesh geometry (verts, edges, faces) all the way, and that means a different approach is worth considering. You've noticed that trying to match up two very different sections of mesh can be quite a  hassle.

Proportional Editing to the rescue!

I'd go for geometry roughly similar to this.



And the use Proportional Edition, move, to push the upper verts into that nice curve. Getting a dome curvature is the smaller problem with this kind of geometry. The biggest issue is thinking ahead about where you want sharp corners and you can do that as a flat surface first and extrude parts down later.

Enable proportional editing and press G to start moving, and Z to exclude the XY movement. Use Shift+Mouse wheel to adjust the sphere of influence. See the manual for more information about proportional editing
. 

The outcome: (with some corrections to the base)